## What is Phaser MR?

Overview. MRage presents a user-friendly and automated frontend to Phaser, but especially difficult cases may require finer control over parameters. The Phaser-MR GUI exposes all options available in the standalone command-line Phaser software, and allows use of additional modes besides MR_AUTO.

**What is log likelihood gain?**

What does LLG stand for? LLG stands for Log Likelihood Gain. The likelihood is the probability that the data would have been measured, given the model, so it allows us to compare how well different models agree with the data.

### Why do we maximize the log likelihood?

The log likelihood This is important because it ensures that the maximum value of the log of the probability occurs at the same point as the original probability function. Therefore we can work with the simpler log-likelihood instead of the original likelihood.

**Why do we use log in MLE?**

So to find the maximum likelihood, it is usually easier to apply a monotone transformation to the likelihood (thus preserving the location of relative extrema) that converts multiplication to addition–this is the logarithm function.

#### Is Bayesian maximum likelihood?

Maximum likelihood estimation (MLE), the frequentist view, and Bayesian estimation, the Bayesian view, are perhaps the two most widely used methods for parameter estimation, the process by which, given some data, we are able to estimate the model that produced that data.

**Can the MLE not exist?**

If the interval included its boundary, then clearly the MLE would be θ = max[Xi]. But since this interval does not include its boundary, the MLE cannot be the maximum, and therefore an MLE does not exist.

## Is EM algorithm monotonic?

It is now intuitively clear that EM based algorithms monotonically increase the data likelihood function, and that they converge with high probability to a local maximum of the likelihood function pZ (z ; θ) that depends on the starting point.

**Why is phase information lost?**

But really what happens is that photons are reflected from the crystal in different directions with a probability proportional to the square of the amplitude of this wave. We count the photons, and we lose any information about the relative phases of different diffraction.

### What is the most common method of solving the phase problem in protein crystallography?

A powerful solution is the Multi-wavelength Anomalous Dispersion (MAD) method. In this technique, atoms’ inner electrons absorb X-rays of particular wavelengths, and reemit the X-rays after a delay, inducing a phase shift in all of the reflections, known as the anomalous dispersion effect.

**Is Bayesian statistics useful for machine learning?**

More specifically, the iterative of Bayesian statistics is very particular in use, it allows data experts to make anticipation more precisely. In present time, Bayesian statistics has a significant role in smart execution of machine learning algorithms as it gives flexibility to data experts to work with big data.

#### Can a likelihood be negative?

Many reliability engineers have the impression that the natural logarithm of the likelihood function (Ln-likelihood) is always negative, or in other words, that the likelihood value should always be less than 0. However, this is not true.

**Are MLE unique?**

The maximum likelihood estimate is shown to exist and to be unique if a twice continuously differentiable likelihood function is constant on the boundary of the parameter space and if the Hessian matrix is negative definite whenever the gradient vector vanishes.

## Should I use Phaser to solve my structure?

Because Phaser implements strategies designed to solve structures with as much confidence as possible, as efficiently as possible, it is best to leave the choice of resolution to Phaser, at least in the first instance. Has Phaser Solved It? Have I solved it? Ideally, a unique solution with a strong signal will be found at the end of the search.

**Can phaser find multiple components in one job?**

It’s a good idea to set up a Phaser run to find all copies of all components in one job, because this allows Phaser to choose the optimal search order and to amalgamate solutions for multiple copies found in one search. Can PHENIX do MRSAD?

### What is the automated mode of phaser?

The automated mode of Phaser is fast when Phaser finds a high Z-score solution to your problem. When Phaser cannot find a solution with a significant Z-score, it “thrashes”, meaning it maintains a list of 100-1000’s of low Z-score potential solutions and tries to improve them.

**What models does phaser use for molecular replacement?**

Phaser must be given the models that it will use for molecular replacement. A model in Phaser is referred to as an “ensemble”, even when it is described by a single file. This is because it is possible to provide a set of aligned structures as an ensemble, from which a statistically-weighted averaged model is calculated.